chr5-56729889-C-T

Variant names:

• chr5-56729889-C-T
• rs12697152

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.641 in 151,858 control chromosomes in the GnomAD database, including 31,978 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31978 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97305 AN: 151740 Hom.: 31962 Cov.: 30

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.648

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.641 AC: 97359 AN: 151858 Hom.: 31978 Cov.: 30 AF XY: 0.641 AC XY: 47518 AN XY: 74176

African (AFR) AF: 0.495 AC: 20499 AN: 41374

American (AMR) AF: 0.678 AC: 10344 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2345 AN: 5154

South Asian (SAS) AF: 0.603 AC: 2889 AN: 4792

European-Finnish (FIN) AF: 0.766 AC: 8073 AN: 10536

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.716 AC: 48674 AN: 67972

Other (OTH) AF: 0.645 AC: 1357 AN: 2104

Alfa AF: 0.681 Hom.: 20111

Bravo AF: 0.628

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12697152; hg19: chr5-56025716;